Evolution and circulation of Yersinia pestis in the Northern Caspian and Northern Aral Sea regions in the 20th-21st centuries

Abstract

According to the whole genome SNP analysis of 38 Yersinia pestis strains isolated in the foci of the Northern Caspian and Northern Aral Sea regions in the 20th–early 21st centuries, between 1912 and 2015, the spatial and temporal structure of the 2.MED population of a medieval biovar in this region was determined. A phylogenetic branch 2.MED4 was identified which preceded the 2.MED1 branch that diverged later. 2.MED1 strains became the etiological agent of high-mortality plague outbreaks that occurred in the Northern Caspian region at the beginning of the 20th century. Later in the 20th century, the 2.MED1 branch became widespread in the Caspian Sea region, Caucasus, and vast areas of Central Asia. Based on the data of phylogenetic analysis, as well as epidemiological and epizootiological data, we reconstructed the paths of spread of the 2.MED1 branch in the Northern Caspian Sea region and in the Northern subzone of the Central Asian deserts. It is shown, that the reason for the activation of plague foci in the Northern Caspian region in the second half of the 20th century after a long inter-epizootic period caused by cyclical climate warming was the return of 2.MED1 from the foci of the Northern Aral Sea region. This led to the formation of stable plague foci in the Northern Caspian Sea region and Pre-Caucasus, which manifested epizootic activity in the second half of the 20th and early 21st centuries.

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

“…Due to this epidemiological significance, these five populations have been sampled over the longest time frames, ranging from 92 years for the Third Pandemic (1.ORI) to 1250 years for the Bronze Age (1.PRE). This affirms the importance of long-term heterochronous sampling for Y. pestis, made possible through the retrieval of ancient DNA 10 and recent sequencing of early 20th century culture collections 31 . By curating and contextualizing this new heterochronous data, we were able to detect temporal signal in extant Y. pestis populations without the use of ancient DNA calibrations for the first time.…”

“…A final limitation is that several populations are curiously excluded from the pandemic nomenclature altogether. For example, Branch 2 populations emerged at the same time as, but separate from, the Second Pandemic and have been associated with high mortality epidemics 31 . In particular, the Medievalis population (2.MED) has dispersed throughout Asia (Fig.…”

“…Even less is known about the Medievalis population whose strains were hypothesized to be responsible for plague outbreaks in the Caspian Sea region which reoccurred throughout the 19th and 20th centuries 31 . We estimated the tMRCA of Medievalis (2.MED) to be between 1560 and 1845 CE, which overlaps with all previously published estimates (Table 1, Supplementary Table S5).…”

Five Draft Genome Sequences of Historical Yersinia pestis Strains of Phylogroups 2.MED4 and 2.MED1 of the Medieval Biovar

“…At the end of the 19th century and beginning of the 20th, numerous outbreaks of plague were registered in the Northern Caspian Sea region in Russia and Kazakhstan. Our studies prove that since 1912, outbreaks in the Northern Caspian Sea region have been caused by Y. pestis strains of the phylogenetic branches 2.MED1 and 2.MED4 of the medieval biovar ( 3 , 4 ). The study of the genomes of the etiological agents of plague outbreaks in the Northern Caspian Sea region at the beginning of the 20th century is important for elucidating the causes of the high mortality rates among the population, as well as for historical reconstruction of the evolution of the medieval biovar of the plague pathogen.…”

Pheno- and genotypic characteristics of Yersinia pestis strains from phylogroups 2.MED4 and 2.MED1 – etiological agents of 20th-century plague outbreaks in the Caspian Sea region

“…Вид Y. pestis включает несколько основных филогенетических линий, одна из которых -2.MED (средневековый биовар) -является возбудителем в очагах чумы в Российской Федерации и сопредельных государствах на общей площади 1959965 км 2 [1,2]. Для штаммов этого биовара характерна экологическая пластичность, его популяции существуют в очагах различного типа: пустынных, полупустынных, горных, высокогорных, равнинных, в том числе и с высокой степенью аридизации, в которых не циркулируют другие биовары и подвиды Y. pestis [1][2][3][4][5]. Согласно историческим данным, наибольшую активность в XX веке Y. pestis проявила в очагах Прикаспийского региона, где в первой половине этого века произошли вспышки чумы с высоким процентом летальности [5].…”